diff --git a/inst/doc/dataRetrieval.pdf b/inst/doc/dataRetrieval.pdf
index 207ffeebf0b083755d7cfc647cf009fd7349198f..d6db7f3751bec57cc99ef3e24ef38b8e8923e57e 100644
Binary files a/inst/doc/dataRetrieval.pdf and b/inst/doc/dataRetrieval.pdf differ
diff --git a/vignettes/dataRetrieval-concordance.tex b/vignettes/dataRetrieval-concordance.tex
index 6531fec293bf5529c291ee7833f0ef8b878bf68a..1c4366a41dd226833944f61227c270b445d18987 100644
--- a/vignettes/dataRetrieval-concordance.tex
+++ b/vignettes/dataRetrieval-concordance.tex
@@ -3,7 +3,7 @@
6 1 8 0 14 1 14 0 24 1 11 0 17 1 20 0 15 1 10 0 5 1 8 %
0 20 1 5 0 16 1 4 0 21 1 10 0 20 1 5 0 4 1 18 0 13 1 %
9 0 26 1 9 0 10 1 10 0 14 1 21 0 19 1 5 0 19 1 5 0 17 %
-1 8 0 14 1 15 0 16 1 5 0 61 1 6 0 14 1 17 0 36 1 5 0 %
-24 1 5 0 20 1 38 0 13 1 10 0 22 1 5 0 5 1 14 0 10 1 5 %
-0 7 1 5 0 16 1 51 0 15 1 49 0 7 1 32 0 26 1 25 0 8 1 %
-5 0 56 1}
+1 8 0 14 1 15 0 16 1 5 0 9 1 5 0 62 1 6 0 14 1 17 0 %
+36 1 5 0 24 1 5 0 20 1 38 0 13 1 10 0 22 1 5 0 5 1 13 %
+0 10 1 5 0 7 1 5 0 16 1 51 0 15 1 49 0 7 1 32 0 26 1 %
+25 0 8 1 5 0 56 1}
diff --git a/vignettes/dataRetrieval.Rnw b/vignettes/dataRetrieval.Rnw
index 11455595d5c818ae8dc8aa61f0325214f677423a..6152ee378a54791bbd614cf583cbbd869887859d 100644
--- a/vignettes/dataRetrieval.Rnw
+++ b/vignettes/dataRetrieval.Rnw
@@ -451,14 +451,24 @@ If there are discharge values of zero, the code will add a small constant to all
%------------------------------------------------------------
\subsection{Sample Data}
%------------------------------------------------------------
-The function to obtain sample data from the water quality portal is getSampleData. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as getRawQWData or getQWData as described in the previous section.
+The function to obtain USGS sample data from the water quality portal is getSampleData. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as getRawQWData or getQWData as described in the previous section.
<<secondExample>>=
parameterCd <- "00618"
Sample <-getSampleData(siteNumber,parameterCd,
- startDate, endDate,interactive=FALSE)
+ startDate, endDate)
+@
+
+The function to obtain STORET sample data from the water quality portal is getSTORETSampleData. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as getRawQWData or getQWData as described in the previous section.
+
+<<STORET,echo=TRUE,eval=FALSE>>=
+site <- 'WIDNR_WQX-10032762'
+characteristicName <- 'Specific conductance'
+Sample <-getSTORETSampleData(site,characteristicName,
+ startDate, endDate)
@
+
\pagebreak
Details of the Sample dataframe are listed below:
diff --git a/vignettes/dataRetrieval.log b/vignettes/dataRetrieval.log
index 44cb50cce9584a679e7239c09aa9183874a946f9..4c618022d6808b402c297b0a1578dbdc9c3b8fd9 100644
--- a/vignettes/dataRetrieval.log
+++ b/vignettes/dataRetrieval.log
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9) (preloaded format=pdflatex 2012.1.6) 17 JUN 2013 15:35
+This is pdfTeX, Version 3.1415926-2.3-1.40.12 (MiKTeX 2.9) (preloaded format=pdflatex 2012.1.6) 27 JUN 2013 15:21
entering extended mode
**dataRetrieval.tex
(D:\LADData\RCode\dataRetrieval\vignettes\dataRetrieval.tex
@@ -671,6 +671,7 @@ Overfull \vbox (21.68121pt too high) has occurred while \output is active []
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+Overfull \hbox (64.3856pt too wide) in paragraph at lines 949--949
[]\OT1/pcr/m/n/10.95 ## First day of the discharge record is 2000-01-01 and la
st day is 2013-01-01[]
[]
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+Overfull \hbox (64.3856pt too wide) in paragraph at lines 949--949
[]\OT1/pcr/m/n/10.95 ## The first sample is from 2000-01-04 and the last sampl
e is from 2012-12-18[]
[]
@@ -717,145 +722,150 @@ e is from 2012-12-18[]
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+<figure/egretEx.pdf, id=310, 505.89pt x 505.89pt>
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+
+Overfull \hbox (70.9556pt too wide) in paragraph at lines 1036--1036
+[]\OT1/pcr/m/n/10.95 ## Sample1 <- localSample[!duplicated(localSample[c("Dec
+Year","ConcHigh")]),][]
+ []
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+Package color Info: Redefining color shadecolor on input line 1047.
+
+Overfull \hbox (90.66557pt too wide) in paragraph at lines 1050--1050
[][]\OT1/pcr/b/n/10.95 install.packages[]\OT1/pcr/m/n/10.95 ([]"dataRetrieval"[
], repos=[]"http://usgs-r.github.com"[], type=[]"source"[])[]
[]
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+Overfull \hbox (157.60596pt too wide) in paragraph at lines 1056--1057
\OT1/ptm/m/n/10.95 C:/Users/userA/Documents/R/win-library/2.15/dataRetrieval, a
nd the de-fault for a Mac: /Users/userA/Library/R/2.15/library/dataRetrieval.
[]
+Package color Info: Redefining color shadecolor on input line 1060.
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[]\OT1/pcr/m/n/10.95 Suspended sediment concentration (SSC) 1980-10-01 1991-09-
30 3651 mg/l[]
[]
-<table1.png, id=356, 554.07pt x 125.71968pt>
+<table1.png, id=360, 554.07pt x 125.71968pt>
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+Underfull \hbox (badness 1983) in paragraph at lines 1346--1347
[]\OT1/ptm/m/n/10.95 Hirsch, R. M., Moyer, D. L. and Arch-field, S. A. (2010),
Weighted Re-gres-sions on
[]
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+Underfull \hbox (badness 1221) in paragraph at lines 1346--1347
\OT1/ptm/m/n/10.95 Time, Dis-charge, and Sea-son (WRTDS), with an Ap-pli-ca-tio
n to Chesa-peake Bay River
[]
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+Underfull \hbox (badness 2443) in paragraph at lines 1346--1347
\OT1/ptm/m/n/10.95 In-puts. JAWRA Jour-nal of the Amer-i-can Wa-ter Re-sources
As-so-ci-a-tion, 46: 857-880.
[]
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+Underfull \hbox (badness 3690) in paragraph at lines 1346--1347
\OT1/ptm/m/n/10.95 doi: 10.1111/j.1752-1688.2010.00482.x []$\OT1/pcr/m/n/10.95
http : / / onlinelibrary . wiley . com / doi /$
[]
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+Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 1353.
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+Output written on dataRetrieval.pdf (33 pages, 291772 bytes).
PDF statistics:
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diff --git a/vignettes/dataRetrieval.synctex.gz b/vignettes/dataRetrieval.synctex.gz
index 3f2d8cbc483300a977cc61b7bd6b9509cb34a01e..158227040e6954c75111acec0006686caa551c35 100644
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diff --git a/vignettes/dataRetrieval.tex b/vignettes/dataRetrieval.tex
index 4a885515a876d8e0a71f64c553a79b56f09dda70..43030a1bf25d08f6d815eb3395f26de03c8daf92 100644
--- a/vignettes/dataRetrieval.tex
+++ b/vignettes/dataRetrieval.tex
@@ -148,7 +148,7 @@ Not every station will measure all parameters. A short list of commonly measured
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Mon Jun 17 15:34:54 2013
+% Thu Jun 27 15:21:30 2013
\begin{table}[ht]
\centering
\begin{tabular}{rll}
@@ -174,7 +174,7 @@ For real-time data, the parameter code and site ID will suffice. For most varia
Some common stat codes are shown in Table \ref{tab:stat}.
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Mon Jun 17 15:34:54 2013
+% Thu Jun 27 15:21:30 2013
\begin{table}[ht]
\centering
\begin{tabular}{rll}
@@ -253,7 +253,7 @@ ChoptankAvailableData <- \hlfunctioncall{getDataAvailability}(siteNumber)
## 2 00010 00001 1988-10-01 2012-05-09 894 dv
## 3 00010 00002 2010-10-01 2012-05-09 529 dv
## 4 00010 00003 2010-10-01 2012-05-09 529 dv
-## 5 00060 00003 1948-01-01 2013-06-16 23908 dv
+## 5 00060 00003 1948-01-01 2013-06-26 23918 dv
## 6 00095 00001 2010-10-01 2012-05-09 527 dv
## 7 00095 00002 2010-10-01 2012-05-09 527 dv
\end{verbatim}
@@ -313,7 +313,7 @@ tableData <- \hlfunctioncall{with}(ChoptankDailyData,
caption=\hlstring{"Daily mean data availabile at the Choptank River"})
\end{alltt}
\end{kframe}% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Mon Jun 17 15:35:00 2013
+% Thu Jun 27 15:21:36 2013
\begin{table}[ht]
\centering
\begin{tabular}{rlllll}
@@ -321,7 +321,7 @@ tableData <- \hlfunctioncall{with}(ChoptankDailyData,
& shortName & Start & End & Count & Units \\
\hline
1 & Temperature, water & 2010-10-01 & 2012-05-09 & 529 & deg C \\
- 2 & Stream flow, mean. daily & 1948-01-01 & 2013-06-16 & 23908 & cfs \\
+ 2 & Stream flow, mean. daily & 1948-01-01 & 2013-06-26 & 23918 & cfs \\
3 & Specific conductance & 2010-10-01 & 2012-05-09 & 527 & uS/cm @25C \\
4 & Suspended sediment concentration (SSC) & 1980-10-01 & 1991-09-30 & 3651 & mg/l \\
5 & Suspended sediment discharge & 1980-10-01 & 1991-09-30 & 3652 & tons/day \\
@@ -682,7 +682,7 @@ Daily <- \hlfunctioncall{getDVData}(siteNumber, \hlstring{"00060"}, startDate, e
Details of the Daily dataframe are listed below:
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Mon Jun 17 15:35:10 2013
+% Thu Jun 27 15:21:46 2013
\begin{table}[ht]
\centering
\begin{tabular}{rllll}
@@ -716,19 +716,34 @@ If there are discharge values of zero, the code will add a small constant to all
%------------------------------------------------------------
\subsection{Sample Data}
%------------------------------------------------------------
-The function to obtain sample data from the water quality portal is getSampleData. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as getRawQWData or getQWData as described in the previous section.
+The function to obtain USGS sample data from the water quality portal is getSampleData. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as getRawQWData or getQWData as described in the previous section.
\begin{knitrout}
\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
\begin{alltt}
parameterCd <- \hlstring{"00618"}
Sample <-\hlfunctioncall{getSampleData}(siteNumber,parameterCd,
- startDate, endDate,interactive=FALSE)
+ startDate, endDate)
+\end{alltt}
+\end{kframe}
+\end{knitrout}
+
+
+The function to obtain STORET sample data from the water quality portal is getSTORETSampleData. The arguments for this function are also siteNumber, ParameterCd, StartDate, EndDate, interactive. These are the same inputs as getRawQWData or getQWData as described in the previous section.
+
+\begin{knitrout}
+\definecolor{shadecolor}{rgb}{0.969, 0.969, 0.969}\color{fgcolor}\begin{kframe}
+\begin{alltt}
+site <- \hlstring{'WIDNR_WQX-10032762'}
+characteristicName <- \hlstring{'Specific conductance'}
+Sample <-\hlfunctioncall{getSTORETSampleData}(site,characteristicName,
+ startDate, endDate)
\end{alltt}
\end{kframe}
\end{knitrout}
+
\pagebreak
Details of the Sample dataframe are listed below:
@@ -776,7 +791,7 @@ As an example to understand how the dataRetrieval package handles a more complex
\begin{center}
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Mon Jun 17 15:35:11 2013
+% Thu Jun 27 15:21:47 2013
\begin{table}[ht]
\centering
\begin{tabular}{rllrlrlr}
@@ -1012,11 +1027,10 @@ To see the raw code for a particular code, type the name of the function:
removeDuplicates
\end{alltt}
\begin{verbatim}
-## function (localSample = Sample)
-## {
-## Sample1 <- localSample[!duplicated(localSample[c("DecYear",
-## "ConcHigh")]), ]
-## return(Sample1)
+## function(localSample=Sample) {
+## Sample1 <- localSample[!duplicated(localSample[c("DecYear","ConcHigh")]),]
+##
+## return(Sample1)
## }
## <environment: namespace:dataRetrieval>
\end{verbatim}
@@ -1062,7 +1076,7 @@ After installing the package, you need to open the library each time you re-star
%------------------------------------------------------------
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Mon Jun 17 15:35:14 2013
+% Thu Jun 27 15:21:50 2013
\begin{table}[ht]
\centering
\begin{tabular}{rl}
@@ -1128,7 +1142,7 @@ After installing the package, you need to open the library each time you re-star
There are 62 columns returned from the water quality portal.
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Mon Jun 17 15:35:14 2013
+% Thu Jun 27 15:21:50 2013
\begin{table}[ht]
\centering
\begin{tabular}{rl}
@@ -1185,7 +1199,7 @@ There are 62 columns returned from the water quality portal.
\FloatBarrier
% latex table generated in R 3.0.1 by xtable 1.7-1 package
-% Mon Jun 17 15:35:14 2013
+% Thu Jun 27 15:21:50 2013
\begin{table}[ht]
\centering
\begin{tabular}{rl}
@@ -1263,7 +1277,7 @@ tableData
## 5 Suspended sediment discharge 1980-10-01
## End Count Units
## 1 2012-05-09 529 deg C
-## 2 2013-06-16 23908 cfs
+## 2 2013-06-26 23918 cfs
## 3 2012-05-09 527 uS/cm @25C
## 4 1991-09-30 3651 mg/l
## 5 1991-09-30 3652 tons/day
diff --git a/vignettes/dataRetrieval.toc b/vignettes/dataRetrieval.toc
index a6398165a491095179565b0083edcdf602e67b5e..8c170c50cc89676b8136c95e7a76963b1962f309 100644
--- a/vignettes/dataRetrieval.toc
+++ b/vignettes/dataRetrieval.toc
@@ -15,16 +15,16 @@
\contentsline {subsection}{\numberline {3.1}INFO Data}{15}{subsection.3.1}
\contentsline {subsection}{\numberline {3.2}Daily Data}{15}{subsection.3.2}
\contentsline {subsection}{\numberline {3.3}Sample Data}{16}{subsection.3.3}
-\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{17}{subsection.3.4}
-\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{18}{subsection.3.5}
-\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{18}{subsubsection.3.5.1}
-\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{19}{subsubsection.3.5.2}
-\contentsline {subsection}{\numberline {3.6}Merge Report}{20}{subsection.3.6}
-\contentsline {subsection}{\numberline {3.7}EGRET Plots}{21}{subsection.3.7}
-\contentsline {section}{\numberline {A}Getting Started in R}{23}{appendix.A}
-\contentsline {subsection}{\numberline {A.1}New to R?}{23}{subsection.A.1}
-\contentsline {subsection}{\numberline {A.2}R User: Installing dataRetrieval}{23}{subsection.A.2}
-\contentsline {section}{\numberline {B}Columns Names}{24}{appendix.B}
-\contentsline {subsection}{\numberline {B.1}INFO dataframe}{24}{subsection.B.1}
-\contentsline {subsection}{\numberline {B.2}Water Quality Portal}{26}{subsection.B.2}
-\contentsline {section}{\numberline {C}Creating tables in Microsoft from R}{29}{appendix.C}
+\contentsline {subsection}{\numberline {3.4}Censored Values: Summation Explanation}{18}{subsection.3.4}
+\contentsline {subsection}{\numberline {3.5}User-Generated Data Files}{19}{subsection.3.5}
+\contentsline {subsubsection}{\numberline {3.5.1}getDailyDataFromFile}{19}{subsubsection.3.5.1}
+\contentsline {subsubsection}{\numberline {3.5.2}getSampleDataFromFile}{20}{subsubsection.3.5.2}
+\contentsline {subsection}{\numberline {3.6}Merge Report}{21}{subsection.3.6}
+\contentsline {subsection}{\numberline {3.7}EGRET Plots}{22}{subsection.3.7}
+\contentsline {section}{\numberline {A}Getting Started in R}{24}{appendix.A}
+\contentsline {subsection}{\numberline {A.1}New to R?}{24}{subsection.A.1}
+\contentsline {subsection}{\numberline {A.2}R User: Installing dataRetrieval}{24}{subsection.A.2}
+\contentsline {section}{\numberline {B}Columns Names}{25}{appendix.B}
+\contentsline {subsection}{\numberline {B.1}INFO dataframe}{25}{subsection.B.1}
+\contentsline {subsection}{\numberline {B.2}Water Quality Portal}{27}{subsection.B.2}
+\contentsline {section}{\numberline {C}Creating tables in Microsoft from R}{30}{appendix.C}
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